Phylum Protozoa: General Characters and Classification
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<I>Chlorella</I> Strain
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Kenneth Nickerson Papers Papers in the Biological Sciences 7-2016 Comparative genomics, transcriptomics, and physiology distinguish symbiotic from free-living Chlorella strains Cristian F. Quispe University of Nebraska-Lincoln, [email protected] Olivia Sonderman University of Nebraska–Lincoln Maya Khasin University of Nebraska–Lincoln, [email protected] Wayne R. Riekhof University of Nebraska–Lincoln, [email protected] James L. Van Etten University of Nebraska-Lincoln, [email protected] SeFoe nelloxtw pa thige fors aaddndition addal aitutionhorsal works at: https://digitalcommons.unl.edu/bioscinickerson Part of the Computational Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Genomics Commons, Marine Biology Commons, Molecular Genetics Commons, Other Genetics and Genomics Commons, Other Life Sciences Commons, Pathogenic Microbiology Commons, and the Plant Pathology Commons Quispe, Cristian F.; Sonderman, Olivia; Khasin, Maya; Riekhof, Wayne R.; Van Etten, James L.; and Nickerson, Kenneth, "Comparative genomics, transcriptomics, and physiology distinguish symbiotic from free-living Chlorella strains" (2016). Kenneth Nickerson Papers. 15. https://digitalcommons.unl.edu/bioscinickerson/15 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Kenneth Nickerson Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, and Kenneth Nickerson This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscinickerson/15 Published in Algal Research 18 (2016), pp 332–340. doi 10.1016/j.algal.2016.06.001 Copyright © 2016 Elsevier B.V. -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. -
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016 April 1981 Revised, May 1982 2nd revision, April 1983 3rd revision, December 1999 4th revision, May 2011 Prepared for U.S. Department of Commerce Ohio Department of Natural Resources National Oceanic and Atmospheric Administration Division of Wildlife Office of Ocean and Coastal Resource Management 2045 Morse Road, Bldg. G Estuarine Reserves Division Columbus, Ohio 1305 East West Highway 43229-6693 Silver Spring, MD 20910 This management plan has been developed in accordance with NOAA regulations, including all provisions for public involvement. It is consistent with the congressional intent of Section 315 of the Coastal Zone Management Act of 1972, as amended, and the provisions of the Ohio Coastal Management Program. OWC NERR Management Plan, 2011 - 2016 Acknowledgements This management plan was prepared by the staff and Advisory Council of the Old Woman Creek National Estuarine Research Reserve (OWC NERR), in collaboration with the Ohio Department of Natural Resources-Division of Wildlife. Participants in the planning process included: Manager, Frank Lopez; Research Coordinator, Dr. David Klarer; Coastal Training Program Coordinator, Heather Elmer; Education Coordinator, Ann Keefe; Education Specialist Phoebe Van Zoest; and Office Assistant, Gloria Pasterak. Other Reserve staff including Dick Boyer and Marje Bernhardt contributed their expertise to numerous planning meetings. The Reserve is grateful for the input and recommendations provided by members of the Old Woman Creek NERR Advisory Council. The Reserve is appreciative of the review, guidance, and council of Division of Wildlife Executive Administrator Dave Scott and the mapping expertise of Keith Lott and the late Steve Barry. -
Pusillus Poseidon's Guide to Protozoa
Pusillus Poseidon’s guide to PROTOZOA GENERAL NOTES ABOUT PROTOZOANS Protozoa are also called protists. The word “protist” is the more general term and includes all types of single-celled eukaryotes, whereas “protozoa” is more often used to describe the protists that are animal-like (as opposed to plant-like or fungi-like). Protists are measured using units called microns. There are 1000 microns in one millimeter. A millimeter is the smallest unit on a metric ruler and can be estimated with your fingers: The traditional way of classifying protists is by the way they look (morphology), by the way they move (mo- tility), and how and what they eat. This gives us terms such as ciliates, flagellates, ameboids, and all those colors of algae. Recently, the classification system has been overhauled and has become immensely complicated. (Infor- mation about DNA is now the primary consideration for classification, rather than how a creature looks or acts.) If you research these creatures on Wikipedia, you will see this new system being used. Bear in mind, however, that the categories are constantly shifting as we learn more and more about protist DNA. Here is a visual overview that might help you understand the wide range of similarities and differences. Some organisms fit into more than one category and some don’t fit well into any category. Always remember that classification is an artificial construct made by humans. The organisms don’t know anything about it and they don’t care what we think! CILIATES Eats anything smaller than Blepharisma looks slightly pink because it Blepharisma itself, even smaller Bleph- makes a red pigment that senses light (simi- arismas. -
Genetic Diversity of Symbiotic Green Algae of Paramecium Bursaria Syngens Originating from Distant Geographical Locations
plants Article Genetic Diversity of Symbiotic Green Algae of Paramecium bursaria Syngens Originating from Distant Geographical Locations Magdalena Greczek-Stachura 1, Patrycja Zagata Le´snicka 1, Sebastian Tarcz 2 , Maria Rautian 3 and Katarzyna Mozd˙ ze˙ ´n 1,* 1 Institute of Biology, Pedagogical University of Krakow, Podchor ˛azych˙ 2, 30-084 Kraków, Poland; [email protected] (M.G.-S.); [email protected] (P.Z.L.) 2 Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland; [email protected] 3 Laboratory of Protistology and Experimental Zoology, Faculty of Biology and Soil Science, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; [email protected] * Correspondence: [email protected] Abstract: Paramecium bursaria (Ehrenberg 1831) is a ciliate species living in a symbiotic relationship with green algae. The aim of the study was to identify green algal symbionts of P. bursaria originating from distant geographical locations and to answer the question of whether the occurrence of en- dosymbiont taxa was correlated with a specific ciliate syngen (sexually separated sibling group). In a comparative analysis, we investigated 43 P. bursaria symbiont strains based on molecular features. Three DNA fragments were sequenced: two from the nuclear genomes—a fragment of the ITS1-5.8S rDNA-ITS2 region and a fragment of the gene encoding large subunit ribosomal RNA (28S rDNA), Citation: Greczek-Stachura, M.; as well as a fragment of the plastid genome comprising the 30rpl36-50infA genes. The analysis of two Le´snicka,P.Z.; Tarcz, S.; Rautian, M.; Mozd˙ ze´n,K.˙ Genetic Diversity of ribosomal sequences showed the presence of 29 haplotypes (haplotype diversity Hd = 0.98736 for Symbiotic Green Algae of Paramecium ITS1-5.8S rDNA-ITS2 and Hd = 0.908 for 28S rDNA) in the former two regions, and 36 haplotypes 0 0 bursaria Syngens Originating from in the 3 rpl36-5 infA gene fragment (Hd = 0.984). -
23.3 Groups of Protists
Chapter 23 | Protists 639 cysts that are a protective, resting stage. Depending on habitat of the species, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no cellular metabolism. Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular stages in both haploid and diploid forms, a strategy called alternation of generations, analogous to that used by plants. Habitats Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay. 23.3 | Groups of Protists By the end of this section, you will be able to do the following: • Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes • Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes • Identify defining features of protists in each of the six supergroups of eukaryotes. In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. -
The Protozoan Nucleus. Molecular and Biochemical Parasitology, 209(1-2), Pp
McCulloch, R., and Navarro, M. (2016) The protozoan nucleus. Molecular and Biochemical Parasitology, 209(1-2), pp. 76-87. (doi:10.1016/j.molbiopara.2016.05.002) This is the author’s final accepted version. There may be differences between this version and the published version. You are advised to consult the publisher’s version if you wish to cite from it. http://eprints.gla.ac.uk/135296/ Deposited on: 22 February 2017 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk *Manuscript Click here to view linked References The protozoan nucleus Richard McCulloch1 and Miguel Navarro2 1. The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, U.K. Telephone: 01413305946 Fax: 01413305422 Email: [email protected] 2. Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Avda. del Conocimiento s/n, 18100 Granada, Spain. Email: [email protected] Correspondence can be sent to either of above authors Keywords: nucleus; mitosis; nuclear envelope; chromosome; DNA replication; gene expression; nucleolus; expression site body 1 Abstract The nucleus is arguably the defining characteristic of eukaryotes, distinguishing their cell organisation from both bacteria and archaea. Though the evolutionary history of the nucleus remains the subject of debate, its emergence differs from several other eukaryotic organelles in that it appears not to have evolved through symbiosis, but by cell membrane elaboration from an archaeal ancestor. Evolution of the nucleus has been accompanied by elaboration of nuclear structures that are intimately linked with most aspects of nuclear genome function, including chromosome organisation, DNA maintenance, replication and segregation, and gene expression controls. -
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. -
I Biology I Lecture Outline 9 Kingdom Protista
I Biology I Lecture Outline 9 Kingdom Protista References (Textbook - pages 373-392, Lab Manual - pages 95-115) Major Characteristics Algae 1. Cbaracteristics 2. Classification 3. Division Cblorophyta 4. Division Chrysophyta 5. Division Phaeopbyta 6. Division Rhodopbyta Protozoans 1. Characteristics 2. Classification 3. Class FlageUata 4. Class Sarcodina 5. Class Ciliata 6. Class Sporozoa I Biology I Lecture Notes 9 Kingdom Protista References (Textbook - pages 373-392, Lab Manual- pages 95-115) Major Characteristics I. Protists possess eukaryotic cells with well defined nuclei and organelles 2. Most are unicellular, however there are multi-cellularforms 3. They are diverse in their structure 4. They vary in size from microscope algae to kelp that can be over 100feet in length 5. They are diverse (like bacteria) in the way they meet their nutritional needs A . Some are photosynthetic like land plants - are autotrophic B. Some ingest theirfood like animals - heterotrophic by ingestion C. Some absorb theirfood like bacteria andfungi - heterotrophic by absorption D. One species - Euglena - is mixotrophic meaning that it is capable ofboth autotrophic and heterotrophic life styles. 6. Reproduction in Protists A. is usually asexual by mitosis B. sexual reproduction involves meiosis and spore formation and usualJy occurs only when environmental conditions are hostile C. spores are resistant and can withstand adverse conditions 7. Some protozoans form cysts - a type ofresting stage 8. Photosynthetic protists (mostly algae) are part ofplankton. Plankton are those organisms suspended infresh and marine waters that serve asfood for -- heterotrophic animals and other protists 9. There are diverse opinions on how to classify members ofthe Kingdom Protista. -
Brown Algae and 4) the Oomycetes (Water Molds)
Protista Classification Excavata The kingdom Protista (in the five kingdom system) contains mostly unicellular eukaryotes. This taxonomic grouping is polyphyletic and based only Alveolates on cellular structure and life styles not on any molecular evidence. Using molecular biology and detailed comparison of cell structure, scientists are now beginning to see evolutionary SAR Stramenopila history in the protists. The ongoing changes in the protest phylogeny are rapidly changing with each new piece of evidence. The following classification suggests 4 “supergroups” within the Rhizaria original Protista kingdom and the taxonomy is still being worked out. This lab is looking at one current hypothesis shown on the right. Some of the organisms are grouped together because Archaeplastida of very strong support and others are controversial. It is important to focus on the characteristics of each clade which explains why they are grouped together. This lab will only look at the groups that Amoebozoans were once included in the Protista kingdom and the other groups (higher plants, fungi, and animals) will be Unikonta examined in future labs. Opisthokonts Protista Classification Excavata Starting with the four “Supergroups”, we will divide the rest into different levels called clades. A Clade is defined as a group of Alveolates biological taxa (as species) that includes all descendants of one common ancestor. Too simplify this process, we have included a cladogram we will be using throughout the SAR Stramenopila course. We will divide or expand parts of the cladogram to emphasize evolutionary relationships. For the protists, we will divide Rhizaria the supergroups into smaller clades assigning them artificial numbers (clade1, clade2, clade3) to establish a grouping at a specific level. -
Environmental Impact Assessment Study Report on Rabindra Sarobar Lake Premises, Kolkata
ENVIRONMENTAL IMPACT ASSESSMENT STUDY REPORT ON RABINDRA SAROBAR LAKE PREMISES, KOLKATA FINAL REPORT APRIL, 2017 Published by West Bengal Pollution Control Board on 05 June 2018 1 EIA Report of Rabindra Sarovar, Kolkata Acknowledgement The West Bengal Pollution Control Board wishes to thank the Hon’ble NGT (EZ) for constituting a five member committee consisting of eminent scientists and engineers to study and submit a report on the probable impact of the activities in the Rabindra Sarovar stadium during the nights, connected with ISL matches, on “physical environment”, “biodiversity of the lake environment” and on the survivability scope of the migratory birds and required preventive measures. The West Bengal Pollution control Board extends heartiest thanks to the expert committee members, constituted to undertake Rapid EIA study in the Rabindra Sarovar: Dr. A.K. Sanyal, Chairman, WBBB (Chairman of the Expert Committee), Dr. Ujjal Kumar Mukhopadhyay, Chief Scientist, WBPCB, Dr. Anirban Roy, Research Officer, WBBB , Dr. Rajib Gogoi, Scientist-D, BSI, Kolkata, Dr. Rita Saha, Scientist-D, CPCB, Kolkata Regional Office, Dr. Deepanjan Majumdar, Sr. Scientist, NEERI, Dr. S.I. Kazmi, Scientist, ZSI, Kolkata and Mr. Ashoke Kumar Das, Secretary, KIT, Kolkata (Convenor). The background information and Literature survey provided by West Bengal Biodiversity Board and Botanical Survey of India were intently helpful to prepare this “ EIA Report of Rabindra Sarovar, Kolkata ” . This could not have been possible to prepare and publish this without their great help. We are also thankful to the team from the West Bengal Biodiversity Board for visiting Rabindra Sarobarlake and premises and contributed their effort & energy to prepare general biodiversity documentation, one of the essential source for this report, with their expertise. -
Reference Database for the 18S Rrna Gene
Received: 3 November 2017 | Revised: 15 February 2018 | Accepted: 24 February 2018 DOI: 10.1111/1755-0998.12781 RESOURCE ARTICLE DINOREF: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene Solenn Mordret1 | Roberta Piredda1 | Daniel Vaulot2 | Marina Montresor1 | Wiebe H. C. F. Kooistra1 | Diana Sarno1 1Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy Abstract 2Sorbonne Universite, CNRS, UMR Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosys- Adaptation et Diversite en Milieu Marin, tems where they occupy various ecological niches. They play a major role as primary Station Biologique, Roscoff, France producers, but many species are mixotrophic or heterotrophic. Environmental Correspondence metabarcoding based on high-throughput sequencing is increasingly applied to Diana Sarno, Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, assess diversity and abundance of planktonic organisms, and reference databases Italy. are definitely needed to taxonomically assign the huge number of sequences. We Email: [email protected] provide an updated 18S rRNA reference database of dinoflagellates: DINOREF. Funding information Sequences were downloaded from GENBANK and filtered based on stringent quality Italian Ministry of Education, University and Research criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. DINOREF includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest num- ber of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. DINOREF provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species.